On 2 Jun 2017, at 14:16, Anthony Dick <adick@fiu.edu> wrote:

Hello Eugenio,

 

Thanks for responding. The PING dataset is a public use dataset but requires direct request from PING. If I share it that would violate the data use agreement: https://pingstudy.ucsd.edu/legal.html. You can get the data but would need to go through the proper channels with PING, and that takes time.

 

However, I could tell you what files are in the MRI directory? Or provide other information that might be helpful? If you know what files the segmentation needs I could possibly just run those specific flags.

 

Anthony

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, June 2, 2017 at 7:10 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] running hippocampal segmentation on PING

 

Dear Anthony,
Can you please send us a sample subject directory (the mri dir is enough, i don't need the surfaces), so i can play with it and see if there's anything we can do?
Cheers
E

Sent from my phone, please excuse brevity and typos

From: Anthony Dick
Sent: Thursday, June 1, 16:40
Subject: [Freesurfer] running hippocampal segmentation on PING
To: Freesurfer support list

Hello,

 

Our group is interested in running the hippocampal segmentation on the PING dataset. That dataset was already Freesurfed, v4.5. When we try to just run the –hippocampal-subfields flag (i.e., recon-all -s bert -hippocampal-subfields-T1) it dies looking for a number of files that were not a part of v.4.5.

 

One option is to start from scratch with v6: recon-all -all -s bert -hippocampal-subfields-T1

 

However, this seems to be a bad option because the quality control on the ~1500 brains is already completed for the original FS run.

 

My question is, are there certain flags from –autorecon2 and –autorecon3 that we could run so we don’t have to re-freesurf everything, or would it be better to just run –all? In other words, what are the minimum files needed to get hippocampal-subfields-T1 to run?

 

Thanks for any suggestions!

 

Anthony

 

—

Anthony Steven Dick, Ph.D.  

Associate Professor

Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience  

Department of Psychology  

Florida International University Modesto A. Maidique Campus AHC4 454  

11200 S.W. 8th Street  

Miami, FL 33199  

Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879  

Email: adick@fiu.edu

Webpage: http://myweb.fiu.edu/adick

Join the Society for the Study of Human Development: http://www.sshdonline.org

 

 

 

 

 

 

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